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Series GSE136328 Query DataSets for GSE136328
Status Public on Mar 01, 2020
Title Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection [II]
Organism Mus musculus
Experiment type Other
Summary CTCF is a key insulator-binding protein and mammalian genomes contain numerous CTCF-binding sites (CBSs), many of which are organized in tandem arrays. Here we provide direct evidence that CBSs, if located between enhancers and promoters in the clustered Pcdh and b-globin clusters, function as an enhancer-blocking insulator by forming distinct directional chromatin loops, regardless whether enhancers contain CBS or not. Moreover, computational simulation and experimental capture revealed balanced promoter usage in vivo in cell populations and stochastic monoallelic expression in single cells by large arrays of tandem variable CBSs. Finally, gene expression levels are negatively correlated with CBS insulators located between enhancers and promoters on a genome-wide scale. Thus, single CBS insulators ensure proper enhancer insulation and promoter activation while tandem-arrayed CBS insulators determine balanced promoter choice. This finding has interesting implications on the role of topological insulators in 3D genome folding and developmental gene regulation.
Overall design QHR-4C profiles of P0 wild type (WT) and CBS-deletion mouse cortex were generated by deep sequencing using Illumina HiSeq X-ten

CBS deletion mouse lines used in this study (UCSC mouse July 2007(mm9) referance genome):
CBSa del chr18:38,001,106-chr18:38,001,113
CBSbcd del chr18:38,011,224-chr18:38,037,839
CBSbc del chr18:38,011,224-chr18:38,013,147
CBSde del chr18:38,036,567-chr18:38,040,872
CBSd del chr18:38,036,568-chr18:38,037,818
CBSb-e del chr18:38011471-chr18:38040871
CBSe del chr18:38,039,423-chr18:38,040,879

Please note that the GSM4046041-GSM4046056 sample records have been moved to GSE211024 on Aug 11, 2022 as per submitter's request.
Contributor(s) Jia Z, Ge X, Wu Y, Wu Q
Citation(s) 32293525
Submission date Aug 26, 2019
Last update date Aug 13, 2022
Contact name Xiao Ge
Organization name Shanghai JiaoTong University
Street address No. 800 Dongchuan Road
City Shanghai
ZIP/Postal code 200240
Country China
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (44)
GSM4045997 4C_p0_cortex_CBSa_a del_rep1
GSM4045998 4C_p0_cortex_CBSa_a del_rep2
GSM4045999 4C_p0_cortex_CBSa_b-e del_rep1
This SubSeries is part of SuperSeries:
GSE138646 Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection
BioProject PRJNA562270
SRA SRP219361

Download family Format
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE136328_RAW.tar 118.1 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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